Age | Commit message (Expand) | Author |
2020-08-31 | Use chroma from guix...* wqflask/wqflask/templates/correlation_matrix.html: Fetch chroma from guix
profile
| BonfaceKilz |
2020-08-31 | Merge pull request #428 from BonfaceKilz/chore/delete-datatables-extensions-f......Delete dataTables and it's extensions from git | BonfaceKilz |
2020-08-31 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
2020-08-29 | Fixed issue where exporting traits would throw an error if a dataset's...group didn't have an InbredSetCode set in the DB
* wqflask/utility/authentication_tools.py - Changed get_group_code to
return an empty string instead of None if InbredSetCode doesn't exist
for a dataset group
* wqflask/wqflask/views.py - Changed zipped export filename to
"export_(datetime)" instead of "collection_(datetime)" since this export
can occur from both the collection page and the global search page
| zsloan |
2020-08-29 | Fixed issue with exporting traits from multiple different groups from...the collection page (the filename wasn't being set)
* wqflask/wqflask/views.py - Set filename to "collection_(datetime)" in
export_traits_csv because it wasn't being set before
| zsloan |
2020-08-28 | Delete dataTables and it's extensions from git...* wqflask/wqflask/static/new/packages/DataTables/: Delete folder.
| BonfaceKilz |
2020-08-28 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
2020-08-27 | Added logic that creates a user account if an e-mail is added to a group...that isn't already associated with a GN2 account and sends the user an
e-mail; still need to test
* wqflask/wqflask/group_manager.py - Added logic sending an invitation
e-mail if user_details aren't found for any of the e-mails provided when
adding users to a group
| zsloan |
2020-08-27 | Added function for sending an invitation e-mail...* wqflask/wqflask/user_login.py - Added send_invitation_email function,
which does what it says
| zsloan |
2020-08-27 | Added manager_user.html because it was missing from git | zsloan |
2020-08-27 | Add check for empty group_code when adding a new resource...* wqflask/utility/authentication_tools.py(add_new_resource): If group_code is
"None", an error is thrown when you try to: `group_code + "_" + str(trait_id)`
| BonfaceKilz |
2020-08-27 | Add a check for a "uuid" object...* wqflask/wqflask/views.py(json_default_handler): Check for "uuid.UUID" instance
to avoid TypeError.
| BonfaceKilz |
2020-08-27 | Update imports...* wqflask/wqflask/api/router.py: Break imports into separate lines and remove
unused ones.
| BonfaceKilz |
2020-08-27 | Remove python2 string processing to utf-8...* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods.
* wqflask/wqflask/search_results.py: Remove utf-8 decode method on string.
| BonfaceKilz |
2020-08-27 | Remove relative imports...* wqflask/runserver.py: Relative imports leads to import errors.
| BonfaceKilz |
2020-08-27 | Replace dict.iteritems() with dict.items()..."iteritems()" got omitted in python3.X
| BonfaceKilz |
2020-08-27 | Convert sibling imports to relative imports...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-import>
| BonfaceKilz |
2020-08-27 | Import "reduce" without a try block...* wqflask/wqflask/correlation_matrix/show_corr_matrix.py: Import 'reduce'
| BonfaceKilz |
2020-08-27 | Replace string arguments to "hmac.new" with bytearray...See: <https://stackoverflow.com/questions/31848293/python3-and-hmac-how-to-handle-string-not-being-binary>
| BonfaceKilz |
2020-08-27 | Fix failing tests | BonfaceKilz |
2020-08-27 | Apply pep-8 formatting | BonfaceKilz |
2020-08-27 | Remove comment block | BonfaceKilz |
2020-08-27 | Replace mysqldb's "escape" with the one from utils.db_tools...Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra
step of converting the binary string to a string.
| BonfaceKilz |
2020-08-27 | Remove redundant methods which are defined elsewhere...* wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are
defined in "utility.db_tools"
| BonfaceKilz |
2020-08-27 | Add global method to convert binary string to plain string...* wqflask/utility/db_tools.py: escape_string returns a binary string which
introduces a bug when composing sql query string. The escaped strings have to be
converted to plain text.
| BonfaceKilz |
2020-08-27 | Remove unused imports | BonfaceKilz |
2020-08-27 | Replace "string.split" & "string.join" with python's inbuilt methods | BonfaceKilz |
2020-08-26 | Remove debug statement...* wqflask/wqflask/views.py(search_page): "debugf" raises an error since the
first arg is expected to be an int
| BonfaceKilz |
2020-08-26 | Remove "from __future__ import new_feature" statements...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
| BonfaceKilz |
2020-08-26 | Replace "__cmp__" with "__eq__" magic method...* wqflask/base/GeneralObject.py: "__cmp__" is no longer used in python3. See:
<https://stackoverflow.com/questions/8276983/why-cant-i-use-the-method-cmp-in-python-3-as-for-python-2>
| BonfaceKilz |
2020-08-26 | Rename "unicode" to "str"...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
| BonfaceKilz |
2020-08-26 | Replace calls to "basestring with "str""...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-basestring>
| BonfaceKilz |
2020-08-26 | Fix failing tests that use python2-htmlgen...* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Fix
tests.
| BonfaceKilz |
2020-08-26 | Replace python2-htmlgen with python-htmlgen...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use
python-htmlgen
| BonfaceKilz |
2020-08-25 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
2020-08-25 | Fixed issue in DatasetType that caused an error when trying to load new...datasets
* wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is
what was causing the error
| zsloan |
2020-08-26 | Update corestats import...* wqflask/utility/Plot.py: import corestats from the utility module.
| BonfaceKilz |
2020-08-26 | Remove unused imports | BonfaceKilz |
2020-08-26 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
2020-08-25 | Merge pull request #427 from BonfaceKilz/Build/add-scientific-js-datatables-p......Build/add scientific js datatables plugin | zsloan |
2020-08-25 | This should fix an issue where the new qtlreaper wouldn't work properlty...with genotypes that only have cM positions
* wqflask/wqflask/marker_regression/qtlreaper_mapping.py -
parse_reaper_output is changed to check if cM and Mb exist in output
when creating marker obs
* wqflask/wqflask/marker_regression/run_mapping.py - Changed
export_mapping_results to properly deal with all combinations of cM and
Mb positions (both and either/or)
| zsloan |
2020-08-25 | Merge pull request #425 from BonfaceKilz/refactor/extract-htmlgen-methods-to-......Refactor/extract htmlgen methods to wrapper class | zsloan |
2020-08-25 | Use scientific.js dataTables extension plugin from guix | BonfaceKilz |
2020-08-24 | Use natural.js dataTables extension plugin from guix | BonfaceKilz |
2020-08-24 | Remove non-keyword args...* wqflask/wqflask/marker_regression/display_mapping_results.py
(HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function
parameters.
| BonfaceKilz |
2020-08-24 | Replace "HtmlGen" method calls with those from "HtmlGenWrapper"...* wqflask/wqflask/marker_regression/display_mapping_results.py
(DisplayMappingResults): Replace direct calls to HtmlGen with methods from
the constructed wrapper class "HtmlGenWrapper".
| BonfaceKilz |
2020-08-24 | Add new wrapper class for HtmlGen method...* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class
| BonfaceKilz |
2020-08-24 | Add tests for the HtmlGenWrapper class...* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add
new tests
| BonfaceKilz |
2020-08-24 | Fix some pylint errors...* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused
imports and add fix some pylint errors
| BonfaceKilz |
2020-08-24 | Remove unused imports...* wqflask/utility/Plot.py: Remove unused imports like "numarray". "numarray" is
does not have py3 support so it's important to remove references to it.
| BonfaceKilz |